I have an '09 stock stage 1, 96" with a PCV with AutoTune. When the outside air temps are cold, around 40 degrees the bike doesn't start. Cranks fine, but won't fire up. I unplugged the PCV and reconnected the stock ecm and it fires up immediatly. Anyone else had this problem?

The first thing I would check is battery voltage, also check voltage drop at crankover. The PC-V requires about 9V to power up and if your battery is marginal and drops voltage excessively it may not be enough to power up the unit.